Phacochoerus africanus, common warthog, whole genome shotgun sequencing project
The common warthog (Phacochoerus africanus) is an endemic, omnivorous species of savanna and woodlands of Sub-Saharan Africa with conservation status of "least-concerned". The species harbour genotypes adapted to the environmental challenges posed by the hot and arid environment as well as by endemic pathogens. Common warthogs are known to be reservoirs of Trypanosoma brucei, the cause of sleeping sickness, and of African Swine Fever, a haemorrhagic disease causing high mortality infections in domestic pigs. While these pathogens cause diseases in humans and pigs, respectively, the warthog hosts appears to be unaffected by them.
For this warthog assembly DNA was isolated from Pulmonary Alveolar Macrophages derived from a single female individual. High molecular weight DNA was sequenced using Pacific Biosciences Sequel instruments at Pacific Biosciences and at Edinburgh Genomics. A total of 44 SMRT cells yielded 150Gbp of raw data with a read N50 of 13.9kbp, providing about 60x coverage of the genome. A contig level assembly was generated using Falcon and Falcon-unzip, reconstructing the 2.4 Gbp long genome in 1,500 contigs (with contig N50 of 3.2Mbp). Scaffolding was done using optical mapping data produced by Deep Seq on a Bionano Saphyr instrument, using Bionano Solve software followed by scaffolding based on proximity ligation method. The Hi-C library was created using Dovetail Genomics' Hi-C library preparation kit. Refining the scaffolds were done with Dovetail Genomics' HiRise pipeline. Gaps in the assembly were filled with PBJelly using the PacBio long-read dataset. Error correction was done with Pilon, based on an Illumina short read library generated from the same warthog individual.
The mitochondrial (MT) DNA was assembled from filtered, MT specific, PacBio long-read sequences using the Flye assembler and was error corrected with Illumina short-read data with Pilon.
Data use: The assembly and associated sequence data are made publicly available by Prof. Alan L. Archibald and colleagues, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK, under the terms of the Toronto Statement (Nature 2009, 461:168) with the following understanding: Users are free to analyse these data if the providers of these data are properly cited, any whole genome analyses should follow guidelines outlined in the Ft. Lauderdale agreement on the use of this assembly and any redistribution of the data should carry this notice. If you are unsure about the use of these data then contact alan.archibald@roslin.ed.ac.uk
Funding sources: BBSRC ISP1 (BBS/E/D/10002070), BBSRC Responsive Mode (BB/S02008X/ Alan Archibald) and the Roslin Foundation.
Long read DNA sequencing: Pacific Biosciences (Menlo Park, California, United States), Edinburgh Genomics (University of Edinburgh, UK)
Short read DNA sequencing: Edinburgh Genomics (University of Edinburgh, UK)
Optical Mapping: Deep Seq, University of Nottingham, UK
Proximity ligation-based scaffolding: Dovetail Genomics, Scotts Valley, CA 95066, United States
Sequence assembly and data integration - The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, UK Less...